def __init__(self,name=None):
self._packets = []
self._jobs = []
if name:
self._name = name
self._path = '/home/ilge/jobs/%s' % self._name
else:
i =0
while True:
i += 1
self._name = '%03d' % i
self._path = '/home/ilge/jobs/%s' % self._name
if not os.path.isdir(self._path):
break
notice('using queue name <%s>' % self._name)
if os.path.isdir(self._path):
notice('removing queue <%s>' % self._path, 'del')
shutil.rmtree(self._path)
os.makedirs(self._path)
def __init__(self, name=None):
self._packets = []
self._jobs = []
if name:
self._name = name
self._path = '/home/ilge/jobs/%s' % self._name
else:
i = 0
while True:
i += 1
self._name = '%03d' % i
self._path = '/home/ilge/jobs/%s' % self._name
if not os.path.isdir(self._path):
break
notice('using queue name <%s>' % self._name)
if os.path.isdir(self._path):
notice('removing queue <%s>' % self._path, 'del')
shutil.rmtree(self._path)
os.makedirs(self._path)
def system(command):
if verbose: notice('running "%s"' % command, 'run')
return os.system(command)
def error(self, message):
notice('Error: %s' % message, 'failed')
sys.exit(2)
def error(self, message):
notice('Error: %s' % message, 'failed')
sys.exit(2)
def system(command):
if verbose: notice('running "%s"' % command, 'run')
return os.system(command)
def submit(self,local=False, cores=1):
cwd = os.getcwd()
if len(self._jobs):
self.finishPacket()
jobs = []
for packet in self._packets:
jobs += packet
group = 1
if len(jobs) > 1100:
group = len(jobs) / 500
walltime = jobs[0].walltime(group)
notice('using group size %d and walltime %s' % (group, walltime))
f = open('%s/job.sh' % self._path, 'w')
f.write('#!/bin/bash\n')
f.write('#PBS -N %s\n' % (self._name))
f.write('#PBS -S /bin/bash\n')
f.write('#PBS -l nodes=1:ppn=%d,mem=%dmb,walltime=%s\n' % (jobs[0].cores(), jobs[0].mem(), walltime))
f.write('#PBS -m a\n')
f.write('#PBS -M %[email protected]\n' % 'ilge')
f.write('#PBS -j oe\n')
f.write('set -e\n')
f.write('set -o pipefail\n')
n = 0
while len(jobs):
f.write('if [ "$PBS_ARRAYID" == %s ]; then\n' % n )
for i in range(0, group):
if not len(jobs): break
job = jobs.pop()
currentPath = '/'.join(job.log().split('/')[:-1])
f.write(' mkdir -p %s 2>&1\n' % currentPath)
f.write(' echo "---------- job started" | tee -a %s\n' % job.log())
f.write(' echo `date`: cd %s 2>&1 | tee -a %s\n' % (currentPath, job.log()))
f.write(' cd %s 2>&1 | tee -a %s\n' % (currentPath, job.log()))
f.write(' cd %s 2>&1\n' % (currentPath))
for path, cmd in job.commands():
if path != currentPath:
f.write(' mkdir -p %s 2>&1 | tee -a %s\n' % (path, job.log()))
f.write(' cd %s 2>&1 | tee -a %s\n' % (path, job.log()))
f.write(' cd %s\n' % (currentPath))
f.write(' echo `date`: cd %s 2>&1 | tee -a %s\n' % (path, job.log()))
currentPath = path
f.write(' echo `date`: \'%s\' 2>&1 | tee -a %s\n' % (cmd.replace('\'', '\'"\'"\''), job.log()))
f.write(' %s 2>&1 | tee -a %s\n' % (cmd, job.log()))
f.write(' echo `date`: "SUCCEEDED" | tee -a %s 2>&1\n' % job.log())
f.write(' #--------------------------------------\n')
f.write(' exit 0\n')
f.write('fi\n')
n += 1
f.close()
notice('queue <%s> contains %d jobs' % (self._name, n))
if local:
notice('computing locally')
for i in range(0,n):
print os.system('PBS_ARRAYID=%d bash %s/job.sh' % (i,self._path)),
else:
notice('submitting queue <%s> to cluster' % self._name)
os.system('ssh lmbtorque "cd /home/ilge/jobs; dir>/dev/null; cd %s; qsub %s/job.sh -t 0-%d"' % (self._path, self._path, n - 1))
os.chdir(cwd)
def submit(self, local=False, cores=1):
cwd = os.getcwd()
if len(self._jobs):
self.finishPacket()
jobs = []
for packet in self._packets:
jobs += packet
group = 1
if len(jobs) > 1100:
group = len(jobs) / 500
walltime = jobs[0].walltime(group)
notice('using group size %d and walltime %s' % (group, walltime))
f = open('%s/job.sh' % self._path, 'w')
f.write('#!/bin/bash\n')
f.write('#PBS -N %s\n' % (self._name))
f.write('#PBS -S /bin/bash\n')
f.write('#PBS -l nodes=1:ppn=%d,mem=%dmb,walltime=%s\n' %
(jobs[0].cores(), jobs[0].mem(), walltime))
f.write('#PBS -m a\n')
f.write('#PBS -M %[email protected]\n' % 'ilge')
f.write('#PBS -j oe\n')
f.write('set -e\n')
f.write('set -o pipefail\n')
n = 0
while len(jobs):
f.write('if [ "$PBS_ARRAYID" == %s ]; then\n' % n)
for i in range(0, group):
if not len(jobs): break
job = jobs.pop()
currentPath = '/'.join(job.log().split('/')[:-1])
f.write(' mkdir -p %s 2>&1\n' % currentPath)
f.write(' echo "---------- job started" | tee -a %s\n' %
job.log())
f.write(' echo `date`: cd %s 2>&1 | tee -a %s\n' %
(currentPath, job.log()))
f.write(' cd %s 2>&1 | tee -a %s\n' %
(currentPath, job.log()))
f.write(' cd %s 2>&1\n' % (currentPath))
for path, cmd in job.commands():
if path != currentPath:
f.write(' mkdir -p %s 2>&1 | tee -a %s\n' %
(path, job.log()))
f.write(' cd %s 2>&1 | tee -a %s\n' %
(path, job.log()))
f.write(' cd %s\n' % (currentPath))
f.write(' echo `date`: cd %s 2>&1 | tee -a %s\n' %
(path, job.log()))
currentPath = path
f.write(' echo `date`: \'%s\' 2>&1 | tee -a %s\n' %
(cmd.replace('\'', '\'"\'"\''), job.log()))
f.write(' %s 2>&1 | tee -a %s\n' % (cmd, job.log()))
f.write(' echo `date`: "SUCCEEDED" | tee -a %s 2>&1\n' %
job.log())
f.write(' #--------------------------------------\n')
f.write(' exit 0\n')
f.write('fi\n')
n += 1
f.close()
notice('queue <%s> contains %d jobs' % (self._name, n))
if local:
notice('computing locally')
for i in range(0, n):
print os.system('PBS_ARRAYID=%d bash %s/job.sh' %
(i, self._path)),
else:
notice('submitting queue <%s> to cluster' % self._name)
os.system(
'ssh lmbtorque "cd /home/ilge/jobs; dir>/dev/null; cd %s; qsub %s/job.sh -t 0-%d"'
% (self._path, self._path, n - 1))
os.chdir(cwd)
